Re: [Dart-help] help with windowlicker

[marcin j. <mar...@gm...>]

Hey there,

The xrate tree job took a while but it seemed to finish without
errors. Alas there isn't any tree output ...

Here's what I get from stdout:

Parsed command line: xrate DvH_DP4_G20_mVISTA.stock -e
/usr2/people/gtl/bin/dart//grammars/jukescantor.eg --noannotate -log 5
Warning -- used random number generator during initialisation
Read 1 alignments
Sequence_database: converting ASCII sequences to score profiles
Estimating tree for the following sequences: CP000112 CP000527 AE017286

The alignment is 3 bacterial genomes, ~3M each -- that wouldn't be a
problem right? And this was run on a hefty machine ...


marcin

On Thu, Apr 24, 2008 at 7:36 PM, marcin joachimiak
<mar...@gm...> wrote:
> much better, thanks!
>  I did notice the trees for each alignment in the output ...
>
>  The tree estimation is running, I'll keep reporting ...
>
>
>
>
>  On Thu, Apr 24, 2008 at 7:22 PM, Ian Holmes <ih...@be...> wrote:
>  > marcin joachimiak wrote:
>  >  > Excellent, its working now!
>  >
>  >  Cool!
>  >
>  >
>  >  > I'll have the tree data soon and may try a run with as well, but best
>  >  > if I could know that the other tree is different from the xrate one
>  >  > with the Jukes-Cantor model. Can I get the Jukes-Cantor model
>  >  > tree/distances from xrate?
>  >
>  >  Yes, it will insert the trees into the alignment files it outputs, using
>  >  the New-Hampshire-encoded-in-Stockholm format from my previous email.
>  >
>  >  One caveat. The way you're running it now, it is calculating a separate
>  >  tree *for every window* in the alignment. This may not be what you want,
>  >  and it's certainly going to slow things down.
>  >
>  >  If you want to calculate the tree just once for the whole alignment, type
>  >
>  >  xrate MY_ALIGNMENT.stock -e $DARTDIR/grammars/jukescantor.eg
>  >  --noannotate -log 5 > MY_ALIGNMENT_WITH_TREE.stock
>  >
>  >
>  >  The "--noannotate" just means "don't waste time trying to annotate this
>  >  alignment, I just want the tree". The "-log 5" will just print some log
>  >  messages on stderr, so you can watch the progress of the tree-building
>  >  algorithms.
>  >
>  >  hth,
>  >
>  >  I.
>  >
>